def temp():
'''Stores ion and electron total temperatures vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_temperatures_%s.txt" % (r), 'a')
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
Ti, Te, _, _ = angle.tmp(i, i)
file.write(str(Ang) + "\t" + str(Ti) + "\t" + str(Te) + "\n")
file.close()
def temp_i():
'''Stores perpendicular and parallel ion temperatures vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti255_ion_temperatures_%s.txt" % (r), 'a')
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
_, _, Tperp, Ei = angle.tmp(i, i)
file.write(str(Ang) + "\t" + str(Tperp) + "\t" + str(2 * Ei) + "\n")
file.close()
def den():
'''Stores density vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_densities_%s.txt" % (r), 'a')
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
n = angle.density(i, i)
file.write(str(Ang) + "\t" + str(n) + "\n")
file.close()
def mag():
'''Stores magnitude of total and poloidal magnetic field vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_magnetic_field_vs.angle_%s.txt" % (r), 'a')
file.write("Angle" + "\t" + "Bp" + "\t" + "B" + "\n")
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
Bp, B = angle.magnetic_field(i, i)
file.write(str(Ang) + "\t" + str(Bp) + "\t" + str(B) + "\n")
file.close()
def dn():
angle.angle_mesh()
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
dn = angle.density_perturbation(i, i)
for t in range(2):
for p in range(core.Nplanes):
file = open("ti255_dn_%s_t_%s_pl_%s.txt" % (r, t, p), 'a')
file.write(str(Ang) + "\t" + str(dn[t, p]) + "\n")
file.close()
def dPe_strength():
'''Stores strength of electron pressure perturbation vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti255_Pe_perturbation_strength_vs.angle_%s.txt" % (r), 'a')
#calls flux function on diagonal points of the mesh
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
dPe = angle.e_pressure_perturbation_strength(i, i)
file.write(str(Ang) + "\t" + str(dPe) + "\n")
file.close()
def dphi_strength():
'''Stores strength of electrostatic fluctuation vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_turbulence_strength_vs.angle_%s.txt" % (r), 'a')
#calls flux function on diagonal points of the mesh
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
_, _, tur = angle.turbulence_strength(i, i)
file.write(str(Ang) + "\t" + str(tur) + "\n")
file.close()
def check():
'''Simple check to see if the values are stored correctly. Useful to see (with verbose option of angle.spline_creation set to true),
if the angular grid covers faithfully the separatrix.
'''
angle.angle_mesh()
file = open("Check_%s.txt" % (r), 'a')
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
file.write(str(Ang) + "\t" + str(R_val) + "\t" + str(Z_val) + "\n")
file.close()
def phis():
'''Stores values potential and electrostatic fluctuation vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_phis_vs.angle_%s.txt" % (r), 'a')
file.write("Angle" + "\t" + "Phi" + "\t" + "dPhi" + "\n")
#calls flux function on diagonal points of the mesh
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
phi, dphi, _ = angle.turbulence_strength(i, i)
file.write(str(Ang) + "\t" + str(phi) + "\t" + str(dphi) + "\n")
file.close()
def dn_strength():
'''Stores strength of density perturbation vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_density_perturbation_strength_vs.angle_%s.txt" % (r),
'a')
#calls flux function on diagonal points of the mesh
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
dn = angle.density_perturbation_strength(i, i)
file.write(str(Ang) + "\t" + str(dn) + "\n")
file.close()
def mag_component():
'''Stores components of magnetic field vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_magnetic_field_comp_vs.angle_%s.txt" % (r), 'a')
file.write("Angle" + "\t" + "Br" + "\t" + "Bz" + "\t" + "Bzeta" + "\n")
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
Br, Bz, Bzeta = angle.mag_comp(i, i)
file.write(
str(Ang) + "\t" + str(Br) + "\t" + str(Bz) + "\t" + str(Bzeta) +
"\n")
file.close()
def main_Tot(Rmin):
angle.angle_mesh()
file = open("ti255_Total_fluxes_vs.angle.txt", 'a')
#calls flux function on diagonal points of the mesh
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
Eq_Gamma_time_avg, Tur_Gamma_time_avg = angle.two_fluxes_angle(
i, i, Ang, 0, Rmin, 3)
file.write(
str(Ang) + "\t" + str(Eq_Gamma_time_avg) + "\t" +
str(Tur_Gamma_time_avg) + "\t" + str(R_val) + "\t" + str(Z_val) +
"\n")
file.close()
def diamagnetic_flux():
'''Stores ion diamagnetic drift fluxes vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_diamag_fluxes_vs.angle_%s.txt" % (r), 'a')
file.write("Angle" + "\t" + "D.Flux" + "\t" + "R" + "\t" + "Z" + "\n")
#calls flux function on diagonal points of the mesh
for i in range(1, len(angle.R_fp) - 2):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
dMag = angle.diamagnetic_drifts_angle(i, i)
file.write(
str(Ang) + "\t" + str(dMag) + "\t" + str(R_val) + "\t" +
str(Z_val) + "\n")
file.close()
def ion_heat_flux():
'''Stores ion exb heat fluxes vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti255_ion_heat_%s.txt" % (r), 'a')
file.write("Angle" + "\t" + "Eq.Flux" + "\t" + "Tur.Flux" + "\t" + "R" +
"\t" + "Z" + "\n")
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
Eq, Tur = angle.ion_heat_flux_angle(i, i, True)
file.write(
str(Ang) + "\t" + str(Eq) + "\t" + str(Tur) + "\t" + str(R_val) +
"\t" + str(Z_val) + "\n")
print("Flux point %s done." % (i))
file.close()
def sl():
'''Stores inverse scale lengths vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti262_Scale_lengths_%s.txt" % (r), 'a')
#calls flux function on diagonal points of the mesh
for i in range(2, len(angle.R_fp) - 2):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
LTe = angle.LTeinv(i, i)
Ln = angle.Lninv(i, i)
LTi = angle.LTiinv(i, i)
file.write(
str(Ang) + "\t" + str(LTe) + "\t" + str(LTi) + "\t" + str(Ln) +
"\t" + str(R_val) + "\t" + str(Z_val) + "\n")
file.close()
def exb_flux():
'''Stores the particle, exb, equilibrium and turbulent fluxes vs. poloidal angle.'''
angle.angle_mesh()
file = open("ti255_particle_fluxes_vs.angle_%s.txt" % (r), 'a')
file.write("Angle" + "\t" + "Eq.Flux" + "\t" + "Tur.Flux" + "\t" + "Ring" +
"\t" + "R" + "\t" + "Z" + "\n")
#calls flux function on diagonal points of the mesh
for i in range(1, len(angle.R_fp) - 1):
R_val = angle.R_fp[i]
Z_val = angle.Z_fp[i]
Ang = angle.norm_atan(Z_val, R_val)
Eq, Tur, Ring = angle.exb_fluxes_angle(i, i, False)
file.write(
str(Ang) + "\t" + str(Eq) + "\t" + str(Tur) + "\t" + str(Ring) +
"\t" + str(R_val) + "\t" + str(Z_val) + "\n")
file.close()
def Re_on_sep(r):
#reading the matrices
Rpol = np.load(
"/global/homes/g/giannos/xgc_python_dir/ti255_analysis/sep_mat/Rsep_%s.npy"
% (r))
Zpol = np.load(
"/global/homes/g/giannos/xgc_python_dir/ti255_analysis/sep_mat/Zsep_%s.npy"
% (r))
arr = np.load(
"/global/homes/g/giannos/xgc_python_dir/ti255_analysis/Reynolds/Re_tur_pol_f_%s.npy"
% (r))
#finding min/max of R,Z.
if ((r * 20) < (len(Rsep) - 1)) and (((r + 1) * 20) < (len(Rsep) - 1)):
Rmin = float(Rsep[r * 20]) #2.14#
Rmax = float(Rsep[(r + 1) * 20]) #2.26#
Zmin = float(Zsep[r * 20]) #-0.38#
Zmax = float(Zsep[(r + 1) * 20]) #0.45#
Rmin, Rmax, Zmin, Zmax = loading_checks(Rmin, Rmax, Zmin, Zmax)
elif ((r * 20) < (len(Rsep) - 1)) and (((r + 1) * 20) > (len(Rsep) - 1)):
Rmin = float(Rsep[r * 20])
Rmax = float(Rsep[-1])
Zmin = float(Zsep[r * 20])
Zmax = float(Zsep[-1])
else:
pass
unitR = (Rmax - Rmin) / 100
unitZ = (Zmax - Zmin) / 100
Zs = np.array([x for x in range(0, arr.shape[0])])
Rs = np.array([x for x in range(0, arr.shape[1])])
file = open(
"/global/homes/g/giannos/xgc_python_dir/ti255_analysis/Reynolds/Re_tur_pol_files_%s.txt"
% (r), 'a')
#file = open("Reynolds_turpf_mid.txt",'a')
#file = open("Reynolds_force_midplane.txt",'a')
#file = open("pol_flow_mid.txt",'a')
#file = open("Re_rad_f_mid.txt",'a')
#file = open("Re_rad_f_mid.txt",'a')
Septrix = list(zip(Rpol, Zpol))
Z_coord = []
Z_loc = []
R_loc = []
R_coord = []
for Z in Zpol:
diff = []
for zeta in Zs:
diff.append(abs(Z -
(zeta * unitZ +
Zmin))) #find units and min/max from parallel.
tmp = np.amin(diff)
Sep_loc_z = diff.index(tmp)
Z_loc.append(Sep_loc_z)
Z_coord.append(Zs[Sep_loc_z] * unitZ + Zmin)
for R in Rpol:
diff = []
for rho in Rs:
diff.append(abs(R - (rho * unitR + Rmin)))
Sep_loc_r = np.argmin(diff)
R_loc.append(Sep_loc_r)
R_coord.append(Rs[Sep_loc_r] * unitR + Rmin - core.Rmaj)
#plt.plot(R_coord,Z_coord,'r--',Rpol,Zpol,'b*')
#plt.show()
#file.write("R"+"\t"+"Z"+"\t"+"Shear"+"\n")
#file.write("R"+"\t"+"Z"+"\t"+"Re_S"+"\n")
file.write("angle" + "\t" + "R" + "\t" + "Z" + "\t" + "Re_rad" + "\n")
coordinates = list(zip(R_coord, Z_coord))
ANG = []
for i in range(0, len(coordinates)):
angie = angle.norm_atan(Z_coord[i], R_coord[i])
ANG.append(angie)
for i in range(0, len(coordinates)):
if arr[Z_loc[i], R_loc[i]] > 0:
file.write(
str(ANG[i]) + "\t" + str(coordinates[i][0]) + "\t" +
str(coordinates[i][1]) + "\t" + str(arr[Z_loc[i], R_loc[i]]) +
"\n")
else:
pass
file.close()
def sh_on_sep(r):
'''For a particular process number, reads in the matrices of R,Z separatrix points, the respective shear matrix and writes out a file
that contains the R,Z,shear information.'''
#reading the matrices
Rpol = np.load("Rsep_%s.npy" % (r))
Zpol = np.load("Zsep_%s.npy" % (r))
arr = np.load("shear_%s.npy" % (r))
#finding min/max of R,Z.
if ((r * 20) < (len(Rsep) - 1)) and (((r + 1) * 20) < (len(Rsep) - 1)):
Rmin = float(Rsep[r * 20]) #2.14#
Rmax = float(Rsep[(r + 1) * 20]) #2.26#
Zmin = float(Zsep[r * 20]) #-0.38#
Zmax = float(Zsep[(r + 1) * 20]) #0.45#
Rmin, Rmax, Zmin, Zmax = loading_checks(Rmin, Rmax, Zmin, Zmax)
elif ((r * 20) < (len(Rsep) - 1)) and (((r + 1) * 20) > (len(Rsep) - 1)):
Rmin = float(Rsep[r * 20])
Rmax = float(Rsep[-1])
Zmin = float(Zsep[r * 20])
Zmax = float(Zsep[-1])
else:
pass
unitR = (Rmax - Rmin) / 100
unitZ = (Zmax - Zmin) / 100
Zs = np.array([x for x in range(0, arr.shape[0])])
Rs = np.array([x for x in range(0, arr.shape[1])])
file = open("shear_files_%s.txt" % (r), 'a')
#file = open("Reynolds_turpf_mid.txt",'a')
#file = open("Reynolds_force_midplane.txt",'a')
#file = open("pol_flow_mid.txt",'a')
#file = open("Re_rad_f_mid.txt",'a')
#file = open("Re_rad_f_mid.txt",'a')
Septrix = list(zip(Rpol, Zpol))
Z_coord = []
Z_loc = []
R_loc = []
R_coord = []
for Z in Zpol:
diff = []
for zeta in Zs:
diff.append(abs(Z -
(zeta * unitZ +
Zmin))) #find units and min/max from parallel.
tmp = np.amin(diff)
Sep_loc_z = diff.index(tmp)
Z_loc.append(Sep_loc_z)
Z_coord.append(Zs[Sep_loc_z] * unitZ + Zmin)
for R in Rpol:
diff = []
for rho in Rs:
diff.append(abs(R - (rho * unitR + Rmin)))
Sep_loc_r = np.argmin(diff)
R_loc.append(Sep_loc_r)
R_coord.append(Rs[Sep_loc_r] * unitR + Rmin - core.Rmaj)
#plt.plot(R_coord,Z_coord,'r--',Rpol,Zpol,'b*')
#plt.show()
#file.write("R"+"\t"+"Z"+"\t"+"Shear"+"\n")
#file.write("R"+"\t"+"Z"+"\t"+"Re_S"+"\n")
file.write("angle" + "\t" + "R" + "\t" + "Z" + "\t" + "shear" + "\n")
coordinates = list(zip(R_coord, Z_coord))
ANG = []
for i in range(0, len(coordinates)):
angie = angle.norm_atan(Z_coord[i], R_coord[i])
ANG.append(angie)
for i in range(0, len(coordinates)):
if arr[Z_loc[i], R_loc[i]] > 0:
file.write(
str(ANG[i]) + "\t" + str(coordinates[i][0]) + "\t" +
str(coordinates[i][1]) + "\t" + str(arr[Z_loc[i], R_loc[i]]) +
"\n")
else:
pass
file.close()
